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JAL-2588 Gap colour scheme now shown in overview
[jalview.git]
/
src
/
jalview
/
gui
/
SequenceRenderer.java
diff --git
a/src/jalview/gui/SequenceRenderer.java
b/src/jalview/gui/SequenceRenderer.java
index
2a2a0cf
..
7a1e263
100755
(executable)
--- a/
src/jalview/gui/SequenceRenderer.java
+++ b/
src/jalview/gui/SequenceRenderer.java
@@
-138,12
+138,20
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
*/
void getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
{
*/
void getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
{
- if (shader != null)
+ if (shader.getColourScheme() != null)
{
{
- resBoxColour = shader.findColour(seq.getCharAt(i),
+ if (forOverview && Comparison.isGap(seq.getCharAt(i))
+ && !shader.getColourScheme().hasGapColour())
+ {
+ resBoxColour = Color.lightGray;
+ }
+ else
+ {
+ resBoxColour = shader.findColour(seq.getCharAt(i),
i, seq);
i, seq);
+ }
}
}
- else if (forOverview && !Comparison.isGap(seq.getCharAt(i)))
+ else if (forOverview && Comparison.isGap(seq.getCharAt(i)))
{
resBoxColour = Color.lightGray;
}
{
resBoxColour = Color.lightGray;
}